Deep within
by XX-Samantha-XX
Summary: Sheppard has found trouble yet again, but what have they imprisoned him for? and who exactly has him?
1. Alone In The Dark

Disclaimer: Characters aren't mine, I think if they were Sheppard would be staying clear of me especially after this fic

Summary: Sheppard has found trouble yet again, but what have they imprisoned him for.

Spoilers: not sure if they will be any yet.

This is set in season 3 so Dr Weir and Dr Beckett are still there, just because I love those characters. This fic maybe pretty dark from the start, so I'm warning you now.

**Deep within **

The air metallic with blood, clinging to his skin and to his every fibre, the smell making him nauseas, he tried to breathe through his mouth but he couldn't, anytime he did his stomach threaten to rebel. Other smells had since faded until all he could smell was blood, death.

Voices were whispering, taunting, blaming him for everything and anything they could, how had they got so much information about him, about Atlantis. The steady voices were cut short only by screams of other prisoners, other people who were trapped just like he was, deep within a planet that nobody had even heard of. When the screams were over the voices returned, which only meant that the voices he heard were all a figment of his subdued imagination.

At first he had tried to reason with his captors, they didn't listen, never did. He had even lost his will to speak; they either ignored him or forced him to watch the next terrifying action they took against another person because of his 'charm'.

They were teaching him a lesson they had said, and boy what a lesson it was. Teaching him not to talk out of turn or someone got hurt, teaching him that his actions had consequences that were too horrible to describe. They were taking his control; his body was slowly shutting down, either from the mental exhaustion or the physical, he wasn't sure anymore, maybe, it was both. His whole body ached with the lessons he had been taught, the wounds weren't life threatening but they hurt all the same, even with his high pain threshold. His mind clung on to the hope of rescue. In the first few days he had tried to escape, but it had failed.

x-X-x

About 3 weeks ago

_Sheppard woke up to the sound of screaming for the third night in a row, he was getting more annoyed if anything. It seemed that people didn't even have to of done much to get locked up in this place, it was morally wrong. He snorted at how much that comment would have made Elizabeth smile. McKay and Ronon would have mostly likely roll their eyes and Teyla would have smile too. _

_He thought about the last time he had seen his friends, they had been running but he couldn't for the life of him remember why or who they were running from. After that, he remember them getting through the gate but obviously he hadn't because the next thing he remembered was waking up to screaming on the first night. _

_It hadn't taken them long after he woke up to come and get him. Two well built goons came for him, clomping along the stone floor, the sounds echoing around, he knew is was worthless to fight, but he just couldn't sit here a do nothing. He ran at the guards as they grabbed him, he head butted the nearest one, turned around and kicked the others knees from under him. That was when a third showed his ugly mug and struck him with a wooden object. All he saw after that was fuzzy images until the darkness claimed him._

_The next time he awoke, he found himself strapped to a chair. His thoughts were a little slow and images were still a little fuzzy, but he could just about make out that he wasn't the only one in this new room. _

"_Hello? Anyone there?" he asked to nobody in particular. Getting no answer he was already getting bored with the setup. _

"_You know, if you think your gonna break me by giving me the silent treatment then your wrong." He taunted a little. As his vision cleared more he could make out the skeleton of a body on a cold metal table. Sheppard got a little scared though didn't show it, he only hoped that they didn't do any experiments on people here. _

_A goon returned to remove the skinless body, Sheppard didn't even bother with the goon, he needed to speak to someone who could get him out. The goon returned moments later and clomped his way over to Sheppard. Sheppard didn't care for the feral look in the guys eyes. The goon grabbed his head and fixed a band across his forehead; he rummaged around in his pockets and found what looked like tape. Sheppard tired to move his head away but the tight band across his head stopped him. The goon that Sheppard had now decided to call caveman forced his eyes open and taped them that way. He moved his head next to Sheppard's ear and whispered dangerously. _

"_Now, all you can do is watch as innocent life is lost because of your earlier actions." Caveman sniggered and waited. _

_Suddenly the door he hadn't noticed was flung open and a man younger than him was strapped to a table. After that Sheppard couldn't remember anything much. What he did remember was that he had been covered in the same man's blood when he had awoken, cold and alone in a different cell. His head spun and he was sick, later that day he was taken to the same room and 'punished' again. _

x-X-x

The gothic arches swirled above him, twisting together, making him dizzy. He tried to block out the other sights he had seen, choosing to concentrate on the solid arches that were all around. The large creature heads on the pillars did nothing to calm his ever growing panic. He tried to see where he had been moved to now, which part of hell he found himself in this time. Strong iron bars around him, restricting his movements to within a four square meter cell. The cold stone beneath him causing him to shudder, however, this wasn't the only thing that caused him to shudder. Crimson stain the floor, just like the other cells he had been in, there was more in this one though, was this the last cell before the end he wondered.

Shouldn't his friends have come for him by now? Hadn't he said enough times that they leave no man behind? How had he even got here? Why couldn't he remember? The voices had also said that his friends no longer cared and that they blamed him too. Usually he wouldn't believe anything his captors had said but this cut him deeply. His friends were his family and obviously they blamed him, why else wouldn't they come and get him. Was this his life now? Well what remained of it anyway.

TBC

_Well what in the world has Sheppard done now and where are his friends, will they find him in time to save him or is it already too late. _


	2. Time

_Sorry for the long wait for the chapter, hope you like it. Thanks for the alerts and reviews so far. _

**Chapter 2 **

The sun stretched across the sky in a lazy arch, it had risen and set to the same sight almost everyday, the person changed but the meaning was the same. Each time one lone figure stood on a pier of the city of the ancestors, the pier was a favourite past time of a lone soldier that had gone missing in action. It wasn't the first time it had happened but the feel of it now made it seem worse, like he was important, and he was, he was the glue that held the people together and stopped the slight difference of the marines and scientists get out of hand. He even helped build the moral.

For each cycle of the sun around where the city lay, the people within hoped that with each coming day they would find that tiniest bit of information that they needed to find their friend, part of their very dysfunctional family. And for each cycle of the night, the people tired to sleep away their worries about the member that had been missing for 30 cycles of the sun around the planet and for the complete cycle of one of the moons.

Dr Weir sighed heavily as she watched the swirl of the water beneath her; she somehow hoped that she would see some semblance of an idea in the calming nature of the waves. Getting none for the millionth time she looked away, not daring to think of the thoughts that said he wasn't coming back. It had already been a month and they were no closer to finding him now, than they had been that first week after endless searches.

The IOA had since all but told her to stop hoping, stop looking, but she couldn't. He wouldn't stop if it were any of the others. He never left anyone behind, so she refused to let the IOA win, she still sent teams on search missions, but the moral and hope on the base was dwindling. They all knew that chances of still being alive after this long, I mean this was the Pegasus galaxy, the odds were, if anything, worse here than they were on earth. At least on Earth they only had one planet to search, here, they had hundreds of planets, ranging from the barren to almost ice age, even prisoner planets, all the ones you only heard about in fantasy books.

Each time they got anything that sparked hope within them, they'd only find themselves at a dead end and it tore them down the more times they tried to hope. The military contingent was surviving, yes, but only just. Major Lorne was doing a great job but it shouldn't be his job to shoulder, they could only hope it was temporary. To hers and others' dismay, Col Caldwell kept trying to change things like he had when John was infected with the wraith nano-virus. Everyone knew that he was only trying to help but the message he was sending, none of them wanted to hear. He was there more often that they liked but they still sent the teams out anytime they got a lead.

Elizabeth knew that the people that were taking this the hardest were his team, she remembered when they had appeared through the gate looking exhausted and close to collapse.

x-X-x

_After hearing the alarms go off, Dr Weir swiftly moved out of her office and down to the gate floor. Taking in the appearance of the number one team, she became worried. They were all barring some minor injuries, that isn't what scared her; it was the looks in their eyes. Even Teyla and Ronon looked shocked at something they had obviously seen, McKay was just silent, that saying more for him than the shock in his eyes and features. Just as the gate shut down she realised that she hadn't seen John. _

"_Where's John?" For a moment she wondered if they had even heard her, they didn't answer, instead the look changed from shock to something she couldn't place. She could feel their hesitation, and she knew before the words left Teyla's mouth. _

"_We do not know." Teyla said calmly. _

"_What happened out there?" Elizabeth questioned, she at least needed to know what happened to them. _

"_What do you think happened? Sheppard pulled his hero act again." A now irate McKay chipped in, she was glad that he'd found his voice but it was the desperation that forced her next question. _

"_What happened to John?" _

"_He…they…said they'd punish him for our transgressions and well took him away, we tried to fight back but they caught us when we tried to run, he went and gave himself up for us. Of all the idiotic things to do he gave himself up to them people." With McKay's triad over, he calmed a little but the intense fear of what them people…no barbarians would do to his friend was still there. They needed to get Sheppard back and quickly. But they knew that as soon as they left the planet that Sheppard would be gone and it would be impossible to find him._

x-X-x

That had been a month ago and still the searches came up empty, the team still continued to look, Teyla asked her contacts if they had heard anything, as did Ronon. McKay did what he usually did when a friend was in trouble and sunk himself into his work, trying to locate Sheppard's locator beacon, searching each grid of space, waiting for the flicker of the signal.

They all had the feeling that he wasn't dead but as the month turned into two and the team started going back on missions, finding supplies for Atlantis and making friends to trade with, they could only wait for anything that may lead them closer to finding their wayward friend.

That same moon had completed two cycles now and the sun saw the lone figure disappear, it only retuned ever couple of nights now, like they had given up on the person as they had given up on that same person's favourite place to go.

Thousands, if not millions of miles away a hunched figure asked himself why he was even still alive, he still hadn't given in to the questions but…he wasn't even sure he knew the answers anymore, the faces, sights and sounds he knew had faded and been replaced by the gothic arches, almost lion looking heads of the creatures, and the now constant screaming in his head.

He still resisted when they came, but he didn't know why. What was it he was fighting for? This was his life wasn't it, the dreams of a city and people that seemed like a family, were just that, a dream. Weren't they?

TBC

_Have they really given up? Has he? Thanks for reading and please review. _


	3. The Simplicity of Words

_Sorry for the long wait for this chapter, hope you enjoy it. _

**Chapter 3- The Simplicity of Words **

"_We've found him."_

Were the only three words she'd been wanting to hear for the past three months.

Three small words, insignificant when separate, but hopeful and joyous when put together in that precise order.

Now that she'd heard them, and the tone that came with them, she wondered whether she was ready to see what was to come.

She wasn't so sure anymore. Yes they needed and wanted him but, would they be able to help him? Would he even want their help anymore?

Unpicking the tone, she found…a sad, almost lost hitch in the voice relaying the information. Usually, coming from Dr McKay she found it more concerning that it had come from Teyla. Teyla was as stoic as the marines and Ronon, but now…the only reason it would sound dejected was if the worst had happened. But it hadn't, _had it?_

No, the voice had said they found him. Yes but, had they said alive.

_No_.

And that is what was weighing her down. They needed Sheppard to be found, to be back; like a plant needed the correct amount of water so the potential was right to keep its structure. Too little and it would shrivel, wilt and die, too much and it would burst then die. Or even forces that needed to balance to create a system in equilibrium.

Rubbing her temples, Elizabeth stood silently in the control room of Atlantis. Though, she'd been here umpteen times before, watching, waiting, wanting them to find something, _anything._

And now they had, she was afraid, afraid that she wouldn't like what she'd see or learn when they stepped through that rippling even horizon. Time seemed to stretch beyond the normal space-time effect, twisting into something longer than any known amount of time…

x-X-x

On the Planet….

Teyla and McKay both couldn't help looking towards their leader, they knew Sheppard wouldn't like being carried, but as far as McKay was concerned he didn't care if Sheppard felt embarrassed by it as long as it got Sheppard home. But _that_ was the problem, even Sheppard in pain and injured would usually perk up enough to argue with being carried like a child.

Now however, just nothing. Allowing them to take his complete weight; without resistance. It was unnatural; like they'd stepped into some parallel universe and found a different Sheppard.

McKay wanted to leave it down to the fact that Sheppard was too tired to care, but he couldn't. Not after how they had found him. Not after how he'd flinch away from any of their touches or movements. McKay's inner voice screamed at him that it was just an illusion; this was Sheppard they were talking about, he was always fine. Wasn't he? Unless, he wasn't.

Sheppard seemed to stir in Ronon's arms, causing Ronon to hold tighter as Sheppard started to thrash…

"_Help me… you have to… help me!" was repeated in his mind, like a broken track. Sometimes broken up by a scream or a sob, sometimes just a silence so absolute it was a vacuum; not even like one, it actually was and each time the sob or scream stopped so did his own breath for that moment one more life was taken away because of him. _

_All because of him. _

_Sheppard fought the urge to scream back saying he knew, oh did he know he had to save them somehow but maybe, just maybe they were the lucky ones this time round. They didn't have to be here anymore. Didn't have to put up with this prison? He used the term lightly, very lightly. It was more a slaughterhouse than anything he'd seen. He'd seen a lot back on Earth but this… _

_Was simply something he'd expect from the wraith or even Kolya, not a somewhat peaceful race of people. _

_And talking meant one more person would die because of him, one more life lost because of his mouth. He wouldn't do that, in fact, he wouldn't actually do anything anymore. _

_They'd taught him that. _

_Nothing but an empty darkness clouded his mind now, blocking everything out while he was sleeping. He didn't even know he'd been rescued by his team. Didn't see the cheerless looks on his friends' faces as they carried him through the shimmering portal to his old home; didn't see anything in his bleak world of dreams that had long since been chased away by the nightmares… _

Almost as soon as the thrashing had started it seemed to stop, they could only wonder what it had been about having seen the place where Sheppard had been held.

The first thing they had noticed about the place where their leader had been held was the large gothic arches, looming over them, making them feel miniscule in comparison. Cobwebs clinging and criss-crossing across the length of the smooth stone. The smell of burning flesh plunged their sense into the decaying depths of a horrific kind of torture. One not seen on earth, well, as far as McKay knew anyway.

Ronon and Teyla hadn't even seemed phased by the gruesomeness of what they had found. They had however, been affected by the sheer amount of bones and fragments lying around, strewn across the floor, just left to linger, as proof of what had been done and what could be done to the people unfortunate enough to have supposedly trespassed against those in command.

The only thing worse than the multitude of bones, was the size of some of them. They ranged from fully grown adults to small, child-like ones. But surely they would subject children to this kind of horrid end. It was just so far beyond wrong that it made McKay almost gag.

Shaking away the thoughts of where they'd found John, McKay walked a little bit a head, getting ready for dialling the gate back home.

But how their friend would be when they got him home, well, that they couldn't imagine. They'd only seen him unconscious so far, the damage unknown.

And they could only hope they'd be able to help their leader to mend what ever had been broken in the time he'd been missing…

TBC

_I know it was a mega short chapter but it means I am still working on this story so please don't give up and please review. I shall try and get the next chapter out ASAP _


	4. Silent Screams

**Chapter 4- Silent Screams**

Elizabeth looked around the table at John's team mates and Beckett; they all looked as exhausted as she felt.

It had been a week since they had come through that shimmering puddle carrying the missing leader...of all things. Carrying the strongest person they all knew back home.

And each of them wished that had been the hardest part over, that now they had him back, things would return to normal like they normally did. But carrying him back without a complaint...that was anything but normal.

While that hadn't been normal, it was understandable. The man was exhausted, malnourished and dehydrated, Beckett had told them as much and they weren't expecting that he would wake that day or maybe even late into the next, his body needed the rest and they were happy to just watch him sleep, elated that they had him back, that he was now safe with people to watch over him. So the team sat for two days in the infirmary, barely sleeping out of concern and needing to believe that he really was back and that it hadn't all been a very elaborate dream.

Pretty much the whole of the city had popped in and out to see how their leader was doing, even the scientist had popped in when they weren't engrossed in work which showed just how much John had done in the three years they had been occupying the city. However, they had expected to see some improvement or some inkling that he would be waking up soon and by the end of the second day their happiness was pushing on the borders of unease.

The third day saw the tides swirling and the skies darkening, where in the previous two the skies had been clear and the tides calm. The third day also saw the feelings of unease crashed into anxiety and the Dr doing more tests to try and understand what was happening in the body of their leader, wondering if he'd missed infection markers or brain damage that could explain what was happening.

The core team were struggling, sleep now eluded them completely and if they had dreamt then it had them waking with a start over possibilities of what could have gone wrong and maybe that this wouldn't be happening if they had just found him sooner, if they had just tried harder to find him. Sure they had been in bad situations before, but this seemed infinitely worse, they was something deep within each of the team telling them that something was wrong and it didn't dissipate even when the doctor returned with all the tests results having been clear of anything that would cause what they were seeing.

Beckett had mumbled to himself and out loud, countless things and numbers that didn't make sense to all of the team but they caught them all the same.

_Airway-Patent and maintaining own...Breathing- Bilateral chest movement, equal, no added sounds on inspiration or expiration. Oxygen saturations 100% and within normal range on gases. Circulation- Pulse 75 and regular, Blood Pressure 125/79. Bloods taken, results normal. PH, O2, CO2, lactate, base excess, haemoglobin etc all within normal ranges._ This continued for minutes and was repeated many a time when the Dr couldn't think of anything else wondering whether they would tell him anything different if he repeated what he knew already.

Sheppard wasn't completely injury free, there were plenty of bruises and scratches and even burns, some of which looked partially healed some fresh but he was keeping an eye on them and they were healing well and weren't infected which was no small miracle when it came to this galaxy. He just couldn't explain it. Although maybe it was just Sheppard's body that needed the rest maybe...well there was nothing else to explain it. _Was there?_

The fourth and fifth day drained their hope from the start of the week and left them with feelings of failure and dread, there wasn't anything more to be done medically for their leader, they refused to leave his side even though the room felt empty and the person lying on the bed no longer looked like the person they knew. Because maybe not all their hope had been diminished. He was a fighter, he was strong and he would come through this.

But the sixth day...

The sixth day brought with it indescribable optimism and a renewed hope.

But it was ripped away so fast and it was so short lived that it was just plain cruel. To anyone else the fact that his eyes had opened would have been cause for celebration, but for his team that knew him so well it was tantamount to torture. Each of them had almost wished that they had found a body, a bad as it sounds, but it meant that their friend would no longer be suffering the torment they could see in his eyes or expression.

Everyone around the table shared bits of the sixth day with the rest so they could get the full picture...

Teyla and Ronan had been watching over their fallen leader when they first saw the signs of him waking, McKay had gone off in search of decent food and Beckett had been in his office.

Teyla immediately, a smile upon her face and speaking softly, had taken hold of John's hand and squeezed it gently to let him know someone friendly was there as he wasn't fully aware yet.

But then the monitors had started increasing in pace and her hand almost burned with the speed John's hand disappeared. Both Teyla and Ronan frowned at this but it wasn't outside the realms of being normal for Sheppard when he'd been capture or tortured before, it could last a few days to weeks before he would let anyone touch him without flinching, depending on what he'd been put through. So it wasn't completely unexpected.

And neither was the lost and confused look in his eyes when he was finally able to open them, after being missing for so long and then asleep for a while anyone was bound to be confused about what had happened.

It was when the Dr had rushed over and started asking questions when they noticed that things were starting to spiral downwards and begun to shatter their hope.

Sheppard's first words depending on the situation were usually 'what happened', 'is the team safe', or 'when can I get out of here' and he at least would humour the Dr and answer the questions he asked if he knew that answering them would get him out of the infirmary faster.

But he didn't speak, didn't make a sound and just continued to stare past anyone that came into his line of sight, as if he was lost to something nobody else could see, and maybe, they thought he was.

The only thing that changed had been that the look of being lost and confusion had turned to torment and fear.

But, that was not the worst of it, his expression seemed contorted into what looked like a scream, if the monitors were beeping then you would think that rigor mortis had set in. What was even more concerning was the scream they could see in his eyes, as if he was trying to scream but couldn't. They'd never seen anything like it, not on somebody living and it seemed to last forever his face only relaxing when the muscles had given up. it had only lasted moment but felt a hell of a lot longer for the ones that had seen it. He's eyes afterwards, were still staring.

Staring but sightless, screaming but silent.

More tests were run when nothing changed hours later but again there was nothing.

All the people that needed to know were made aware of the new situation and were told not to let it spread amongst the masses just yet. All they needed to know was that Sheppard was being looked after.

The people that did know, were lost themselves, they didn't know what to do or how to fix this. Beckett was researching anything and everything about psychology as he thought that is where the problems lay and knew that after he was told about how they had found Sheppard, that there was going to be some struggles in the future but he hadn't expected anything of this magnitude, sure he'd heard about it but he wouldn't wish it upon anyone he knew. But then they didn't know what Sheppard had been through on that god forsaken planet for the three months he'd been there. And therein lay the issue, if they didn't know, they couldn't help.

It was now the seventh day and they were sat at a conference table, trying to pool all their knowledge and expertise into how to help Sheppard. None of the people were saying anything about the fact that if this continued then Sheppard would be sent back to earth and that they would have a fight on their hands about being told to get back to work. None of them wanted that, not ever and they would fight if it came down to it.

x-X-x

For a split second, Sheppard had thought he'd heard Teyla's soft voice in the distance but he'd hear it before and it had been an illusion that time so probably was this time as well. He felt the touch of a hand on his for a moment before he pulled it away, if it had been Teyla he might have known for a split second but his mind pulled him away into the depths of the hell swirling around his mind.

_Hands...cold...skeletal...slippery...fleshy..._

_The all encompassing smell of blood and fear wasn't new the Sheppard, neither was the chemical smell of something acidic that he'd seen burn through flesh, fat and muscle until there remained only bones. He'd even gotten used to the sickly smell of freshly dead and decaying bodies. These seemed a constant in his life at the moment. _

_The sounds that had become constant were enough to drive anyone crazy, the screaming, the sobbing, sounds coming from different directions around him of all the ways these people had to kill, maim and hurt. But half the time he swore that most of the sounds were stuck on repeat in only his mind because when he had dared to look around at each of the rooms he had been in he hadn't seen anyone being tortured or hurt or maimed. The other half of the time the evidence for the sound was right in front of him bleeding to death or melting like waxwork models through the cracks of the cold stone beneath him._

_Something was different though, something he couldn't place...well maybe if you opened your eyes then you'd be able to see it his mind taunted. _

_But hundreds of images that he knew he would never forget had already been burnt into his retinas and into his mind and most of it hadn't been by choice so now that he had that control back then he chose not to look anymore. He was tired, tired of seeing the horrors of where ever in the hell he was. He'd been left for a while now though he didn't know quite how much time had passed, no one had taken him away to be tortured some more or had failed to force information out of him. That was the only thing that he'd had any control over so he wouldn't give in. He knew that whether he spoke or not someone would be killed, it didn't matter to these monsters. It was just fun for these people._

_Not that he had any idea of the day or how long he'd been here but he knew that it was stretching into weeks now with his escape attempts all having failed and no sign of rescue, he couldn't remember the day where he'd given up hope of being found but it had happened somewhere along the way and he knew it had involved lots of death even if he couldn't or his warped brain wouldn't remember the details he knew that there was a snowballs chance in hell that any kind of a rescue would succeed. _

_Eyes tightly shut against seeing anything he moved his hands and felt around to see if he could determine anything without looking..._

_He froze and pulled his hand away as if it had been burnt._

_But the rest of his numb body starting to awaken was beginning to confirm what his hand had just told him...the softness that came with either a quilt or flesh...the slickness that he had come to know as blood, especially in this place...the bony prominences in particular places..._

_His breath hitched as his heart rate started to sore and before he knew it acidic bile was racing up to escape his malnourished body so he had to turn the side so he wouldn't choke._

_His head was spinning as his eyes opened of their own volition, looking at the horror before him and not being able to look away. _

**TBC**

_So what are they going to do? Will the team be forced to send Shep home if he doesnt get better? What did Shep see when he opened his eyes? Will his team be able to help him or is he too far gone? Stay tuned for next time !_

_I know this story has been gone for like...ever but alas i have resurrected it and hopefully should be able to get somewhere with it as i had been struggling with ideas for it. _


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